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Elucidating Ribosomal Translocation with Internal Coordinate Flexible Fitting
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
2014 (English)In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, 492A-493A p.Article in journal, Meeting abstract (Other academic) Published
Abstract [en]

Determining conformational changes of large macromolecules is challenging experimentally and computationally. The ribosome has been observed crystallographically in several states but many others have been seen only by low-resolution methods including cryo-electron microscopy. Meanwhile the crucial dynamics between states remain out of reach of experimental structure determination methods. Most existing computational approaches model complexes at all-atom resolution, at very high cost, or use approximations which lose some of the most interesting dynamical details. I have developed Internal Coordinate Flexible Fitting (ICFF), a multiscale method that uses full atomic forces and flexibility only in key regions of a model, capturing extensive conformational rearrangements at low cost. I use ICFF to turn low-resolution density maps, crystallographic structures, and biochemical information into the largest-scale all-atoms trajectory of ribosomal translocation modeled to date. ICFF is three orders of magnitude faster than the most comparable existing method. The results suggest an intriguing possible mechanism of translocation.

Place, publisher, year, edition, pages
2014. Vol. 106, no 2, 492A-493A p.
National Category
Biophysics
Identifiers
URN: urn:nbn:se:uu:diva-228604DOI: 10.1016/j.bpj.2013.11.2754ISI: 000337000402727OAI: oai:DiVA.org:uu-228604DiVA: diva2:734558
Conference
58th Annual Meeting of the Biophysical-Society, FEB 15-19, 2014, San Francisco, CA
Available from: 2014-07-18 Created: 2014-07-17 Last updated: 2017-12-05Bibliographically approved

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Flores, Samuel C.

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